17-19585538-A-G

Position:

• chr17-19585538-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420951.1(ENSG00000290454):​n.272+5203A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,912 control chromosomes in the GnomAD database, including 13,827 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (13827 hom., cov: 31)
• Consequence: ENST00000420951.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

(HGNC:):

SLC47A1P1 (HGNC:51849): (SLC47A1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000420951.1	n.272+5203A>G		intron_variant, non_coding_transcript_variant		5
SLC47A1P1	ENST00000449666.3	n.348-1086A>G		intron_variant, non_coding_transcript_variant
	ENST00000574267.1	n.26+12359T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000454535.5	n.129+3983A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63574 AN: 151792 Hom.: 13795 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.418

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.419 AC: 63656 AN: 151912 Hom.: 13827 Cov.: 31 AF XY: 0.423 AC XY: 31379 AN XY: 74250

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.420

Alfa AF: 0.388 Hom.: 26194

Bravo AF: 0.436

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.0
DANN	Benign	0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2453589; hg19: chr17-19488851;